Place the pecans in a food processor and pulse until they reach a coarse flour consistency. Be careful not to over-process, or you'll end up with pecan butter! Add the coconut flour and salt, pulsing briefly to combine. In a separate bowl, whisk together the maple syrup, egg, vanilla, and melted coconut oil. Pour this wet mixture into the food processor and pulse until a sticky dough forms.
Press the pecan mixture evenly into a 9-inch pie dish, working from the center outward and up the sides. Use the back of a measuring cup to help create an even layer. If the dough seems too sticky, slightly dampen your fingers with cold water. Place the formed crust in the refrigerator while preparing the filling.
Peel, core, and slice the apples into ¼-inch thick pieces. Immediately toss them with lemon juice in a large bowl to prevent browning. In a small bowl, mix together the coconut sugar, arrowroot starch, cinnamon, nutmeg, cloves, and salt. Sprinkle this mixture over the apples and toss until evenly coated.
Heat a large, deep skillet over medium heat. Add the ghee or coconut oil. Once melted, add the seasoned apples and cook for 8-10 minutes, stirring occasionally, until the apples start to soften but still retain some firmness. Remove from heat and stir in the vanilla extract. Allow the mixture to cool for 10 minutes.
Preheat your oven to 350°F (175°C). Remove the crust from the refrigerator and arrange the cooled apple filling in the center. For an optional decorative touch, arrange a few thin apple slices in a pattern on top. Cover the pie edges with aluminum foil or a pie shield to prevent burning. Bake for 25 minutes, then remove the foil and continue baking for 20-25 more minutes, until the crust is golden and the filling is bubbling.
Allow the pie to cool on a wire rack for at least 30 minutes before serving. This cooling period is crucial for the filling to set properly. For clean slices, waiting 1-2 hours is ideal.